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I think the main reason is convenience. If people only hack ruby, fire red and maybe emerald then you need to download (illegally...) 2 or 3 ROMS rather than the full 5 to cover all possible hacks.
The cubone would require a little bit of ASM - have a look at:
http://bulbapedia.bulbagarden.net/wiki/Pok%C3%A9mon_data_substructures_in_the_GBA
and
http://bulbapedia.bulbagarden.net/wiki/Pok%C3%A9mon_data_structure_in_the_GBA
For the headbutt trees, try asking zel as he made them in Shiny...
I find it kind of irritating when people say "Oh, emerald isn't unstable at all". Yes it is. I'm sorry, but weeeird things happen in it for absolutely no reason. Like once I was inserting some tiles. Everything seemed fine, I clicked save and immediately and irreversibly every single tile in the...
Hmm... You should get this moved to the "Progressing Hack" section as this really isn't just an idea, it's an actual hack. Anyway, it looks good, although it's hard to tell how good the mapping will be from the restricted samples here. Good luck, though!
XSE and Pokéscript are in the scripting section already.
Well, I'm sceptical of how useful A-Text is. I rarely use it except to edit things I don't know where the pointer is for (e.g. Introduction, Start Menu, Multi-choice boxes).
I'll change it to moderate if someone else agrees with you.